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Manganese in PDB 8jq3: Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus

Protein crystallography data

The structure of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus, PDB code: 8jq3 was solved by H.Yoshida, A.Yoshihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.51 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.7, 139.94, 147.31, 90, 90, 90
R / Rfree (%) 16 / 21.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus (pdb code 8jq3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus, PDB code: 8jq3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8jq3

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Manganese binding site 1 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:38.9
occ:1.00
 OE2 A:GLU228 2.2 29.4 1.0
OD2 A:ASP261 2.3 23.2 1.0
ND1 A:HIS288 2.3 29.7 1.0
OD2 A:ASP328 2.4 35.3 1.0
CD A:GLU228 3.0 25.7 1.0
OE1 A:GLU228 3.2 26.1 1.0
CG A:ASP261 3.2 21.1 1.0
CE1 A:HIS288 3.3 29.6 1.0
CG A:HIS288 3.3 28.0 1.0
CG A:ASP328 3.4 34.1 1.0
CB A:ASP261 3.4 21.4 1.0
CB A:HIS288 3.6 27.8 1.0
CB A:ASP328 3.7 28.5 1.0
O A:HOH687 3.9 29.8 1.0
CE1 A:HIS264 4.2 26.4 1.0
CG A:GLU228 4.3 23.9 1.0
OD1 A:ASP261 4.4 23.2 1.0
NE2 A:HIS288 4.4 27.4 1.0
CD2 A:HIS288 4.5 27.1 1.0
OD1 A:ASP328 4.5 38.3 1.0
CA A:ASP261 4.6 21.3 1.0
ND1 A:HIS264 4.7 25.8 1.0
NE2 A:HIS264 4.8 25.0 1.0
CG2 A:THR259 4.9 22.0 1.0

Manganese binding site 2 out of 8 in 8jq3

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Manganese binding site 2 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:26.0
occ:1.00
 OD1 A:ASP296 2.0 25.2 1.0
O A:HOH687 2.0 29.8 1.0
O A:HOH602 2.0 39.3 1.0
OD1 A:ASP298 2.1 28.3 1.0
NE2 A:HIS264 2.2 25.0 1.0
O A:HOH609 2.2 33.1 1.0
CG A:ASP296 2.8 28.0 1.0
CD2 A:HIS264 3.0 24.3 1.0
OD2 A:ASP296 3.0 29.5 1.0
CG A:ASP298 3.1 25.8 1.0
CE1 A:HIS264 3.3 26.4 1.0
OD2 A:ASP298 3.5 30.9 1.0
O A:HOH732 3.9 33.1 1.0
OD2 A:ASP261 4.0 23.2 1.0
OD1 A:ASP261 4.1 23.2 1.0
CG A:HIS264 4.2 23.3 1.0
CB A:ASP296 4.2 26.1 1.0
ND1 A:HIS264 4.3 25.8 1.0
CG A:ASP261 4.3 21.1 1.0
OG A:SER290 4.3 21.8 1.0
CB A:ASP298 4.4 23.6 1.0
O A:ASP296 4.7 27.0 1.0
CA A:ASP298 4.8 21.5 1.0
CA A:ASP296 4.8 24.6 1.0
C A:ASP296 4.8 24.4 1.0
N A:ASP298 4.8 20.9 1.0

Manganese binding site 3 out of 8 in 8jq3

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Manganese binding site 3 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:34.8
occ:1.00
 OD2 B:ASP328 2.2 34.1 1.0
OE2 B:GLU228 2.2 26.7 1.0
ND1 B:HIS288 2.2 26.3 1.0
OD2 B:ASP261 2.3 27.0 1.0
CD B:GLU228 3.0 23.7 1.0
CE1 B:HIS288 3.2 29.7 1.0
CG B:HIS288 3.2 26.3 1.0
OE1 B:GLU228 3.2 26.6 1.0
CG B:ASP261 3.2 21.2 1.0
CG B:ASP328 3.2 31.3 1.0
CB B:ASP261 3.4 20.6 1.0
CB B:HIS288 3.5 22.8 1.0
O B:HOH614 3.6 34.2 1.0
CB B:ASP328 3.6 25.9 1.0
CE1 B:HIS264 4.1 26.1 1.0
CG B:GLU228 4.3 21.5 1.0
NE2 B:HIS288 4.3 29.1 1.0
OD1 B:ASP328 4.4 40.3 1.0
CD2 B:HIS288 4.4 26.9 1.0
OD1 B:ASP261 4.4 23.2 1.0
CA B:ASP261 4.6 19.5 1.0
ND1 B:HIS264 4.7 24.0 1.0
NE2 B:HIS264 4.8 26.3 1.0
CG2 B:THR259 4.8 19.1 1.0

Manganese binding site 4 out of 8 in 8jq3

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Manganese binding site 4 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:27.2
occ:1.00
 O B:HOH601 1.8 31.9 1.0
O B:HOH695 2.0 32.7 1.0
NE2 B:HIS264 2.1 26.3 1.0
O B:HOH614 2.1 34.2 1.0
OD1 B:ASP296 2.1 25.8 1.0
OD1 B:ASP298 2.2 23.9 1.0
CG B:ASP296 2.9 25.3 1.0
CD2 B:HIS264 3.0 25.1 1.0
OD2 B:ASP296 3.0 28.1 1.0
CG B:ASP298 3.2 22.8 1.0
CE1 B:HIS264 3.2 26.1 1.0
OD2 B:ASP298 3.5 22.5 1.0
O B:HOH709 3.8 22.7 1.0
OD2 B:ASP261 3.9 27.0 1.0
CG B:HIS264 4.2 24.4 1.0
OD1 B:ASP261 4.2 23.2 1.0
O B:HOH641 4.2 27.8 1.0
ND1 B:HIS264 4.3 24.0 1.0
CG B:ASP261 4.3 21.2 1.0
CB B:ASP296 4.3 26.3 1.0
OG B:SER290 4.4 21.2 1.0
CB B:ASP298 4.5 22.1 1.0
O B:ASP296 4.7 26.2 1.0
CA B:ASP298 4.8 20.4 1.0
C B:ASP296 4.9 23.5 1.0
CA B:ASP296 4.9 25.5 1.0
N B:ASP298 4.9 21.2 1.0

Manganese binding site 5 out of 8 in 8jq3

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Manganese binding site 5 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:35.3
occ:1.00
 OD2 C:ASP261 2.2 24.4 1.0
OD2 C:ASP328 2.3 40.3 1.0
ND1 C:HIS288 2.3 25.1 1.0
OE2 C:GLU228 2.3 27.7 1.0
CD C:GLU228 3.0 24.1 1.0
CG C:ASP261 3.2 22.4 1.0
OE1 C:GLU228 3.2 23.7 1.0
CG C:HIS288 3.3 25.4 1.0
CG C:ASP328 3.3 32.5 1.0
CE1 C:HIS288 3.3 28.1 1.0
CB C:ASP261 3.4 21.5 1.0
CB C:HIS288 3.5 23.9 1.0
CB C:ASP328 3.6 26.6 1.0
O C:HOH614 4.0 25.3 1.0
CE1 C:HIS264 4.1 23.4 1.0
OD1 C:ASP261 4.3 23.1 1.0
CG C:GLU228 4.3 24.4 1.0
NE2 C:HIS288 4.4 29.8 1.0
CD2 C:HIS288 4.4 27.4 1.0
OD1 C:ASP328 4.4 36.4 1.0
CA C:ASP261 4.6 20.0 1.0
ND1 C:HIS264 4.7 23.6 1.0
NE2 C:HIS264 4.8 24.5 1.0
CG2 C:THR259 4.9 22.1 1.0
CA C:HIS288 5.0 23.0 1.0

Manganese binding site 6 out of 8 in 8jq3

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Manganese binding site 6 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:24.2
occ:1.00
 O C:HOH614 1.9 25.3 1.0
O C:HOH616 2.0 29.5 1.0
OD1 C:ASP296 2.0 27.8 1.0
OD1 C:ASP298 2.1 24.5 1.0
O C:HOH619 2.2 30.1 1.0
NE2 C:HIS264 2.2 24.5 1.0
CG C:ASP296 2.8 26.4 1.0
OD2 C:ASP296 2.9 29.1 1.0
CD2 C:HIS264 3.0 23.1 1.0
CG C:ASP298 3.1 24.8 1.0
CE1 C:HIS264 3.3 23.4 1.0
OD2 C:ASP298 3.4 23.9 1.0
O C:HOH746 4.0 26.8 1.0
OD1 C:ASP261 4.1 23.1 1.0
OD2 C:ASP261 4.1 24.4 1.0
CB C:ASP296 4.2 26.9 1.0
CG C:HIS264 4.2 22.5 1.0
ND1 C:HIS264 4.3 23.6 1.0
OG C:SER290 4.4 20.8 1.0
CG C:ASP261 4.4 22.4 1.0
CB C:ASP298 4.4 25.5 1.0
O C:ASP296 4.6 24.0 1.0
CA C:ASP298 4.8 22.7 1.0
C C:ASP296 4.8 23.9 1.0
CA C:ASP296 4.8 25.7 1.0
N C:ASP298 4.9 21.8 1.0
OD2 C:ASP328 5.0 40.3 1.0

Manganese binding site 7 out of 8 in 8jq3

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Manganese binding site 7 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:37.3
occ:1.00
 ND1 D:HIS288 2.2 25.8 1.0
OD2 D:ASP261 2.3 22.1 1.0
OD2 D:ASP328 2.4 46.1 1.0
OE2 D:GLU228 2.4 26.4 1.0
CD D:GLU228 3.0 24.9 1.0
CE1 D:HIS288 3.1 28.9 1.0
OE1 D:GLU228 3.2 27.7 1.0
CG D:ASP261 3.2 20.0 1.0
CG D:HIS288 3.3 24.8 1.0
CG D:ASP328 3.3 36.4 1.0
CB D:ASP261 3.5 20.0 1.0
CB D:HIS288 3.6 22.8 1.0
CB D:ASP328 3.6 30.1 1.0
O D:HOH710 3.9 31.4 1.0
CE1 D:HIS264 4.2 23.6 1.0
NE2 D:HIS288 4.3 29.8 1.0
CG D:GLU228 4.3 23.7 1.0
CD2 D:HIS288 4.4 27.3 1.0
OD1 D:ASP261 4.4 21.4 1.0
OD1 D:ASP328 4.5 39.8 1.0
CA D:ASP261 4.6 20.0 1.0
NE2 D:HIS264 4.8 23.5 1.0
ND1 D:HIS264 4.8 23.9 1.0
CG2 D:THR259 4.9 19.3 1.0

Manganese binding site 8 out of 8 in 8jq3

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Manganese binding site 8 out of 8 in the Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of L-Rhamnose Isomerase From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:26.3
occ:1.00
 OD1 D:ASP296 2.0 27.6 1.0
O D:HOH609 2.0 30.6 1.0
O D:HOH710 2.1 31.4 1.0
O D:HOH623 2.1 31.6 1.0
OD1 D:ASP298 2.1 24.6 1.0
NE2 D:HIS264 2.4 23.5 1.0
CG D:ASP296 2.9 27.6 1.0
CG D:ASP298 3.1 24.8 1.0
OD2 D:ASP296 3.1 28.5 1.0
CD2 D:HIS264 3.1 23.3 1.0
OD2 D:ASP298 3.4 28.8 1.0
CE1 D:HIS264 3.5 23.6 1.0
O D:HOH738 3.8 25.2 1.0
OD2 D:ASP261 4.1 22.1 1.0
OD1 D:ASP261 4.2 21.4 1.0
O D:HOH671 4.2 33.8 1.0
CB D:ASP296 4.3 26.1 1.0
OG D:SER290 4.3 21.1 1.0
CG D:HIS264 4.3 21.9 1.0
CG D:ASP261 4.4 20.0 1.0
CB D:ASP298 4.4 23.3 1.0
ND1 D:HIS264 4.5 23.9 1.0
O D:ASP296 4.7 24.6 1.0
CA D:ASP298 4.7 22.2 1.0
N D:ASP298 4.8 22.2 1.0
CA D:ASP296 4.8 25.1 1.0
C D:ASP296 4.8 24.4 1.0

Reference:

H.Yoshida, N.Yamamoto, L.H.Kurahara, K.Izumori, A.Yoshihara. X-Ray Structure and Characterization of A Probiotic Lactobacillus Rhamnosus Probio-M9 L-Rhamnose Isomerase. Appl.Microbiol.Biotechnol. V. 108 249 2024.
ISSN: ESSN 1432-0614
PubMed: 38430263
DOI: 10.1007/S00253-024-13075-9
Page generated: Sun Oct 6 13:20:47 2024

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